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Prognosis: Not Good

Unless you have a backup, if you've written data to the disk, you're probably not going to be able to recover the files without some good technical skills (the links above provide a variety of different methods of doing it based on your circumstances).

Your best bet would be to copy off your important stuff to a backup, reinstall the OS and restore the needed files from the backup you just created.

Anything else is risky as you don't have a list of the files that were deleted to know if you've got them all recovered/restored or not. This can result in system instability, possible server security issues and other possibly bad things that come with not knowing for sure if your server is working correctly or not.